Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum

İnce, Ayşe Gül; Karaca, Mehmet

doi:10.1007/s10265-021-01287-3

Cited by 6 publications

(12 citation statements)

References 60 publications

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“…Consequently, there is a huge need for new biochemical or molecular markers of seed viability that improve the process of monitoring plant material during storage in gene banks and to help with the understanding of the concomitant aging process occurring in seeds. These studies have developed rapidly over the last decade and substantiate the importance of volatile organic compounds [ 94 , 95 , 98 ], proteomic studies [ 191 ], RNA integrity [ 192 , 193 , 194 , 195 , 196 ] and DNA damage markers or epigenetic marks [ 96 , 97 , 99 , 190 , 197 , 198 , 199 , 200 ] that are highly promising and should be more widely explored.…”

Section: Discussionmentioning

confidence: 99%

Choosing the Right Path for the Successful Storage of Seeds

Trusiak

Plitta-Michalak

Michalak

2022

Plants

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Seeds are the most commonly used source of storage material to preserve the genetic diversity of plants. However, prior to the deposition of seeds in gene banks, several questions need to be addressed. Here, we illustrate the scheme that can be used to ensure that the most optimal conditions are identified to enable the long-term storage of seeds. The main questions that need to be answered pertain to the production of viable seeds by plants, the availability of proper protocols for dormancy alleviation and germination, seed tolerance to desiccation and cold storage at −20 °C. Finally, it is very important to fully understand the capability or lack thereof for seeds or their explants to tolerate cryogenic conditions. The proper storage regimes for orthodox, intermediate and recalcitrant seeds are discussed.

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Section: Discussionmentioning

confidence: 99%

Choosing the Right Path for the Successful Storage of Seeds

Trusiak

Plitta-Michalak

Michalak

2022

Plants

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“…Different methylation patterns may also persist in later developmental stages to facilitate long-term adaptation to metal-contaminated sites [91]. DNA methylation can orchestrate significant changes to plant physiology, especially at earlier stages of plant development [94]. Genes were ranked based on Log2 FC from each pairwise comparison.…”

Section: Deg Analysis Reveals Different Patterns Of Gene Expression B...mentioning

confidence: 99%

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

Moy,

Nkongolo

2024

Plants

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The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

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“…Using the Primer 3 program (Untergasser et al, 2012), degenerate primer pairs were created depending on the following primary parameters: The predicted amplified product size was defined as 400-800 bp, the annealing temperature (Ta) as 58°C-62°C, and the GC content value as 40%-80%. Following design, Y (C/T) was used to replace the cytosine bases (C) in the forward primers and R (A/G) was used to replace the guanine bases (G) in the reverse primers (Ince et al, 2010b;Ince and Karaca, 2021).…”

Section: Target Dna Sequencesmentioning

confidence: 99%

“…A comparative analysis of the genomes of various Capsicum species revealed that the large appearance of leucine-rich domain protein (NLR) genes by retroduplication could give rise to functional nucleotide-binding (Kim et al, 2017). Up to date, methylation-sensitive amplified polymorphism (MSAP), gas chromatographic method, high-performance liquid chromatography (HPLC), and bisulfite sequencing have been used in pepper (Potris et al, 2004;Xu et al, 2015;Shams et al, 2020;Ince and Karaca, 2021;Araz et al, 2022;Cai et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Novel methylation specific bisulfite primer pairs for epigenetic studies of Capsicum spp.

INCE,

KARACA

2023

International Journal of Agriculture Environment and Food Sciences

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Over the past ten years, interest in epigenetic has rapidly increased. Heritable and stable changes in gene expression without any change in DNA sequence is in the field of epigenetics. Plants have a well-preserved epigenetic signature called DNA methylation. It is an essential epigenetic mark that protects genomic stability, silences harmful transposon insertions, and controls global gene expression in all developmental stages and environmental circumstances. All three sequence contexts, the asymmetric CpHpH context and the symmetric CpG and CpHpG contexts (where H is C, A, or T), are among DNA methylation sites in plants. Particularly, DNA cytosine methylation affects a wide range of biological processes, such as gene expression, chromatin structure, DNA packing, recombination, genomic imprinting, and DNA replication. The choice of primer pairs that flank cytosine methylation contexts is critical when designing for the detection of DNA cytosine methylation using bisulfite sequencing. We have developed and synthesized 26 bisulfite specific primer pairs suitable for DNA cytosine methylation investigations in peppers. These primers are specific to certain promoters, intergenic regions, and gene bodies (exons, introns, and UTRs). DNA samples taken from various tissues and developmental stages of Capsicum annuum L. Demre Sivrisi were analyzed by these primer pairs to confirm their utilization.

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Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum

Cited by 6 publications

References 60 publications

Choosing the Right Path for the Successful Storage of Seeds

Choosing the Right Path for the Successful Storage of Seeds

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

Novel methylation specific bisulfite primer pairs for epigenetic studies of Capsicum spp.

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